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Old 01-09-2012, 10:26 AM   #3
Location: RTP

Join Date: Aug 2011
Posts: 12

I am using Joe Pickrell's data (, which I believe are single end reads, and have been running them as such using the following settings.

> time tophat -r 200 -p 14 -o tophat_out_s_1 /illumina/runs/data/bowtie_indexes/hg19.ebwt.zip_FILES/hg19 s_1_sequence.fastq

so, I have been working with s_1, s_3, s_5, and s_7. each from different samples/individual.
From your message, I would continue to run each seperately through tophat.
At the Cufflinks stage, do you prefer to cuffmerge, and then run cuffdiff, or some other set of steps?
many thanks!
hmortens is offline   Reply With Quote